Systems biology of protein quality control
While important work has been done studying the individual components of protein quality control pathways, much remains unknown about how they work in combination to protect cells from defective proteins. The Brandman Lab has approached this problem from an engineering perspective, creating quantitative in vivo molecular probes and systems genetic approaches tools to parse pathways of protein quality control into inputs, sensors, and outputs and to identify the genes and molecular pathways that mediate them.
For four decades the availability of free chaperones has been proposed to regulate the HSR, a transcriptional program which regulates the expression of chaperones. Yet chaperone availability and the HSR had never been quantified in tandem in cells under stress conditions, so the degree to which this mechanism was used in vivo remained unknown. We created a reporter system in yeast to quantify the availability of Hsp90 chaperone in vivo and found that the HSR is indeed regulated under multiple stress conditions by availability of Hsp90, with independent regulation by the Hsp70 chaperone system (Alford and Brandman, 2018). Thus, the HSR responds to diverse defects in protein quality by monitoring the state of multiple chaperone systems concurrently and independently.
The availability of cellular chaperones drives the heat shock response
The ubiquitin-proteasome system adapts to proteolytic and folding stressors via independent mechanisms
We assessed the performance and adaptability of the UPS under proteotoxic stress conditions by creating quantitative readouts of UPS performance and adaptation (Work and Brandman, 2019). We found that impairing the rate at which proteasomes degrade substrates (“proteolytic stress”) or inducing protein misfolding (“folding stress”) stabilizes misfolded proteins through separate mechanisms. The former directly blocks degradation of misfolded proteins whereas the latter results in their aggregation rather than their targeting to the proteasome. Despite this difference, the UPS productively adapts to both proteolytic and folding stressors by upregulating its components. Adaptation is so effective that virtually no loss in performance of protein degradation of model substrates is observed under some stress conditions (“perfect” adaptation). Our results demonstrate the extent to which the UPS adapts to different types of stress and the underlying regulatory mechanisms by which this adaptation occurs. Our studies of both the HSR and the UPS use systems approaches to discover novel ensemble behavior and mechanistic phenomenon, a strategy which offers promise for approaching complex problems across biology.
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